ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs.

ABSTRACT: We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four caref

SUBMITTER: Cleves AE 

PROVIDER: S-EPMC5429375 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature